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JobManagementAdvanced
A parametric job allows to submit a set of jobs in one submission command by specifying parameters for each job.
- To define this parameter the attribute Parameters must be defined in the JDL, the values that it can take are:
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- A list (strings or numbers).
- Or, an integer, in this case the attributes ParameterStart and ParameterStep must be defined as integers to create the list of job parameters.
A simple example is to define the list of parameters using a list of values, this list can contain integers or strings::
Executable = "testJob.sh";
JobName = "%s_parametric";
Arguments = "%s";
Parameters = {"first","second","third","fourth","fifth"};
StdOutput = "StdOut_%s";
StdError = "StdErr_%s";
InputSandbox = {"testJob.sh"};
OutputSandbox = {"StdOut_%s","StdErr_%s"};
In this example, 5 jobs will be created corresponding to the Parameters list values. Note that other JDL attributes can contain "%s" placeholder. For each generated job this placeholder will be replaced by one of the values in the Parameters list.
In the next example, the JDL attribute values are used to create a list of 20 numbers starting from 1 (ParameterStart) with a step 2 (ParameterStep)::
Executable = "testParametricJob.sh";
JobName = "Parametric_%n";
Arguments = "%s";
Parameters = 20;
ParameterStart = 1;
ParameterStep = 2;
ParameterFactor = 1;
StdOutput = "StdOut_%j";
StdError = "StdErr_%j";
InputSandbox = {"testJob.sh"};
OutputSandbox = {"StdOut_%j","StdErr_%j"};
Therefore, with this JDL job description 20 jobs will be submitted in at once. As in the previous example, the "%s" placeholder will be replaced by one of the parameter values. Note the new placeholders: %n is replaced by the Parameter sequential number ( 0,1,2,... ); %j is replaced by the DIRAC JobID.
Parametric jobs are submitted as normal jobs, the command output will be a list of the generated job IDs, for example::
$ dirac-wms-job-submit Param.jdl JobID = [1047, 1048, 1049, 1050, 1051]
These are standard DIRAC jobs. The jobs outputs can be retrieved as usual specifying the job IDs::
$ dirac-wms-job-get-output 1047 1048 1049 1050 1051
Message Passing Interface (MPI) is commonly used to handle the communications between tasks in parallel applications. Two versions and implementations supported in DIRAC are the following::
- MPICH-1 : MPICH1 - MPICH-2 : MPICH2
Users should know that, currently, the MPI jobs can only run on one grid site. So, the maximum number of processors that a user can require for a job depends on the capacity and the policy of the sites.
Another important point, is that some applications need all nodes to work with a shared directory, in some cases, sites provide such a shared disk space but not always.
To define MPI jobs using DIRAC it is necessary:
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Create a wrapper script, this script prepares the environment variables, the arguments are the mpi program without extension c, for example::
$ more application.sh #!/bin/bash EXECUTABLE=$1 NUMPROC=$2 DOMAIN=`hostname -f|cut -d. -f2-10` MPICC=`which mpicc` MPIRUN=`which mpirun` MPIH=`which mpi.h` # Optional echo "=========================================" echo "DATE: " `/bin/date` echo "Domain: " $DOMAIN echo "Executable: " $EXECUTABLE echo "Num Proc: " $NUMPROC echo "MPICC: " $MPICC echo "MPIRUN: " $MPIRUN echo "MPIH: " $MPIH echo "MPI_SHARED_HOME: " `echo $MPI_SHARED_HOME` echo "=========================================" export x=`echo $MPI_SHARED_HOME` echo "Starting MPI script" mpdtrace if [ $? -eq 0 ]; then mpicc -o $EXECUTABLE.o ./EXECUTABLE.c -lm if [[ -z "$x" || "$x" == "no" ]]; then DIR=$HOME/$TMP_DIR export PATH=$PATH:$DIR for i in `mpdtrace`; do ssh $i.$DOMAIN mkdir -p $DIR scp $PWD/$EXECUTABLE* $i.$DOMAIN:$DIR/; ssh $i.$DOMAIN ls -la $DIR done; else DIR=$MPI_SHARED_HOME/$TMP_DIR mkdir $DIR cp $EXECUTABLE.o $DIR; fi $MPIRUN -np $NUMPROC $DIR/$EXECUTABLE.o x=`echo $MPI_SHARED_HOME`; if [[ -z "$x" || "$x" == "no" ]]; then for i in `mpdtrace`; do ssh $i.$DOMAIN 'rm -rf $DIR'; done; else cd .. rm -rf $DIR fi else exit fi -
Edit the JDL: - Set the JobType attribute to "MPI" - Set Flavor attribute to specify which version of MPI libraries you want to use - MPICH2 or MPICH1 - Set CPUNumber attribute
For example::
JobType = "MPI"; CPUNumber = 2; Executable = "application.sh"; Arguments = "mpifile 2 "; StdOutput = "StdOut"; StdError = "StdErr"; InputSandbox = {"application.sh","mpifile.c","inputfile.txt"}; OutputSandbox = {"mpifile.o","StdErr","StdOut"}; Flavor = "MPICH2"
MPI Jobs are submitted as normal jobs, for example::
$ dirac-wms-job-submit mpi.jdl JobID = 1099
To retrieve the job outputs use a usual dirac-wms-job-get-output command::
$ dirac-wms-job-get-output 1099
The DIRAC API is encapsulated in several Python classes designed to be used easily by users to access a large fraction of the DIRAC functionality. Using the API classes it is easy to write small scripts or applications to manage user jobs and data.
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First step, create a Python script specifying job requirements.
Test-API.py:
from DIRAC.Core.Base import Script Script.parseCommandLine() from DIRAC.Interfaces.API.Dirac import Dirac from DIRAC.Interfaces.API.Job import Job j = Job() j.setCPUTime(500) j.setExecutable('echo',arguments='hello') j.setExecutable('ls',arguments='-l') j.setExecutable('echo', arguments='hello again') j.setName('API') dirac = Dirac() result = dirac.submit(j) print 'Submission Result: ',result -
Send the Job using the script:
python Test-API.py $ python testAPI.py {'OK': True, 'Value': 196}
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Create a script Status-API.py:
from DIRAC.Core.Base import Script Script.parseCommandLine() from DIRAC.Interfaces.API.Dirac import Dirac from DIRAC.Interfaces.API.Job import Job import sys dirac = Dirac() jobid = sys.argv[1] print dirac.status(jobid)
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Execute script:
python Status-API.py <Job_ID> $python Status-API.py 196 {'OK': True, 'Value': {196: {'Status': 'Done', 'MinorStatus': 'Execution Complete', 'Site': 'LCG.IRES.fr'}}}
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Example Output-API.py:
from DIRAC.Core.Base import Script Script.parseCommandLine() from DIRAC.Interfaces.API.Dirac import Dirac from DIRAC.Interfaces.API.Job import Job import sys dirac = Dirac() jobid = sys.argv[1] print dirac.getOutputSandbox(jobid) print dirac.getJobOutputData(jobid)
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Execute script:
python Output-API.py <Job_ID> $python Output-API.py 196
The Local submission mode is a very useful tool to check the sanity of your job before submission to the Grid. The job executable is run locally in exactly the same way ( same input, same output ) as it will do on the Grid Worker Node. This allows to debug the job in a friendly local environment.
Let's perform this exercise in the python shell.
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Load python shell:
bash-3.2$ python Python 2.5.5 (r255:77872, Mar 25 2010, 14:17:52) [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from DIRAC.Core.Base import Script >>> Script.parseCommandLine() >>> from DIRAC.Interfaces.API.Dirac import Dirac >>> from DIRAC.Interfaces.API.Job import Job >>> j = Job() >>> j.setExecutable('echo', arguments='hello') {'OK': True, 'Value': ''} >>> Dirac().submit(j,mode='local') 2010-10-22 14:41:51 UTC /DiracAPI INFO: <=====DIRAC v5r10-pre2=====> 2010-10-22 14:41:51 UTC /DiracAPI INFO: Executing workflow locally without WMS submission 2010-10-22 14:41:51 UTC /DiracAPI INFO: Executing at /afs/in2p3.fr/home/h/hamar/Tests/APIs/Local/Local_zbDHRe_JobDir 2010-10-22 14:41:51 UTC /DiracAPI INFO: Preparing environment for site DIRAC.Client.fr to execute job 2010-10-22 14:41:51 UTC /DiracAPI INFO: Attempting to submit job to local site: DIRAC.Client.fr 2010-10-22 14:41:51 UTC /DiracAPI INFO: Executing: /afs/in2p3.fr/home/h/hamar/DIRAC5/scripts/dirac-jobexec jobDescription.xml -o LogLevel=info Executing StepInstance RunScriptStep1 of type ScriptStep1 ['ScriptStep1'] StepInstance creating module instance ScriptStep1 of type Script 2010-10-22 14:41:53 UTC dirac-jobexec.py/Script INFO: Script Module Instance Name: CodeSegment 2010-10-22 14:41:53 UTC dirac-jobexec.py/Script INFO: Command is: /bin/echo hello 2010-10-22 14:41:53 UTC dirac-jobexec.py/Script INFO: /bin/echo hello execution completed with status 0 2010-10-22 14:41:53 UTC dirac-jobexec.py/Script INFO: Output written to Script1_CodeOutput.log, execution complete. 2010-10-22 14:41:53 UTC /DiracAPI INFO: Standard output written to std.out {'OK': True, 'Value': 'Execution completed successfully'} -
Exit python shell
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List the directory where you run the python shell, the outputs must be automatically created:
bash-3.2$ ls Local_zbDHRe_JobDir Script1_CodeOutput.log std.err std.out bash-3.2$ more Script1_CodeOutput.log <<<<<<<<<< echo hello Standard Output >>>>>>>>>> hello
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Create a Test-API-Multiple.py script, for example:
from DIRAC.Core.Base import Script Script.parseCommandLine() from DIRAC.Interfaces.API.Dirac import Dirac from DIRAC.Interfaces.API.Job import Job j = Job() j.setCPUTime(500) j.setExecutable('echo',arguments='hello') for i in range(5): j.setName('API_%d' % i) dirac = Dirac() jobID = dirac.submit(j) print 'Submission Result: ',jobID -
Execute the script:
$ python Test-API-Multiple.py Submission Result: {'OK': True, 'Value': 176} Submission Result: {'OK': True, 'Value': 177} Submission Result: {'OK': True, 'Value': 178}
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Create a Test-API-JDL.py:
from DIRAC.Core.Base import Script Script.parseCommandLine() from DIRAC.Interfaces.API.Job import Job j = Job() j.setName('APItoJDL') j.setOutputSandbox(['*.log','summary.data']) j.setInputData(['/vo.formation.idgrilles.fr/user/v/vhamar/test.txt','/vo.formation.idgrilles.fr/user/v/vhamar/test2.txt']) j.setOutputData(['/vo.formation.idgrilles.fr/user/v/vhamar/output1.data','/vo.formation.idgrilles.fr/user/v/vhamar/output2.data'],OutputPath='MyFirstAnalysis') j.setSystemConfig("") j.setCPUTime(21600) j.setDestination('LCG.IN2P3.fr') j.setBannedSites(['LCG.ABCD.fr','LCG.EFGH.fr']) j.setLogLevel('DEBUG') j.setExecutionEnv({'MYVARIABLE':'TEST'}) j.setExecutable('echo',arguments='$MYVARIABLE') print j._toJDL() -
Run the API:
$ python Test-API-JDL.py Origin = "DIRAC"; Priority = "1"; Executable = "$DIRACROOT/scripts/dirac-jobexec"; ExecutionEnvironment = "MYVARIABLE=TEST"; StdError = "std.err"; LogLevel = "DEBUG"; BannedSites = { "LCG.ABCD.fr", "LCG.EFGH.fr" }; StdOutput = "std.out"; Site = "LCG.IN2P3.fr"; SystemConfig = ""; OutputPath = "MyFirstAnalysis"; InputSandbox = "jobDescription.xml"; Arguments = "jobDescription.xml -o LogLevel=DEBUG"; JobGroup = "vo.formation.idgrilles.fr"; OutputSandbox = { "*.log", "summary.data", "Script1_CodeOutput.log", "std.err", "std.out" }; MaxCPUTime = "21600"; JobName = "APItoJDL"; InputData = { "LFN:/vo.formation.idgrilles.fr/user/v/vhamar/test.txt", "LFN:/vo.formation.idgrilles.fr/user/v/vhamar/test2.txt" }; JobType = "User";
As you can see the parameters added to the job object are represented in the JDL job description. It can now be used together with the dirac-wms-job-submit command line tool.
The complete API documentation can be found here